Eastern Clade Research Articles

Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii)

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor ∼1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley’s Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

A new frog species (Myobatrachidae: Uperoleia) from the Northern Deserts region of Australia, with a redescription of U. trachyderma.

The frog genus Uperoleia (Myobatrachidae) is species rich, with the greatest diversity in the northern monsoonal region of Australia. Due in part to their small body size, conservative morphology and distribution in diverse habitats, the genus is likely to harbor cryptic species. A recent study (Catullo et al. 2013) assessed region-wide genetic, acoustic and phenotypic variation within four species in northern Australia. Catullo et al. (2013) presented multiple lines of evidence that the widespread U. trachyderma comprises distinct allopatric western and eastern lineages within the Northern Deserts bioregion of Australia. Here we formally describe the western lineage as U. stridera sp. nov. and redescribe the eastern (type) clade as U. trachyderma. The new species can be distinguished from U. trachyderma by fewer pulses per call, a faster pulse rate, and the lack of scattered orange to red flecks on the dorsum. The description of U. stridera sp. nov. brings the number of Uperoleia species to 28, by far the largest genus in the Myobatrachidae, and further highlights the Australian monsoonal tropics as a region of high endemism.

Genetic structure of Bufo bankorensis distinguished by amplified restriction fragment length polymorphism of cytochrome b

Abstract Background Bufo bankorensis is an endemic species in Taiwan, and its populations are geographically and reproductively isolated. However, the distinction of Taiwanese B. bankorensis as a separate species from the Chinese Bufo gargarizans remains in dispute. Results A primer set was designed to explore the mitochondrial (mt)DNA cytochrome (Cyt) b sequence (700 bp) of B. bankorensis in 148 individuals collected from 12 locations in Taiwan. After a polymerase chain reaction and sequencing, we found that the nucleotide sequence of Cyt b contained two restricted enzyme sites of Bam HI and Tsp RI. Following Bam HI enzyme digestion, samples of B. bankorensis were divided into two clades: western (which were undigested) and eastern (which were digested) clades. Additionally, Cyt b of the western clade of B. bankorensis was not cut by Bam HI, while it was cut by Tsp RI into two sublineages. The result infers that at least two broadly divergent phylogroups of B. bankorensis exist in Taiwan and are not morphologically distinguishable. Based on the divergent sequence of Cyt b and cutting restriction enzymes, these populations were classified into three distinct phylogroups. Conclusion Genetically, one (western group 1, uncut by Bam HI and cut by Tsp RI) is most likely B. gargarizans, a second one (western group 2, uncut by both Bam HI and Tsp RI) is B. bankorensis, and a third one (eastern clade, cut by Bam HI but not cut by Tsp RI) could be a new subspecies. All three phylogroups were found in some areas, suggesting that they are sympatric, not allopatric.

Intraspecific Phylogeny and Nucleotide Diversity of the Least Shrews, theSorex minutissimus-S. yukonicusComplex, Based on Nucleotide Sequences of the Mitochondrial CytochromebGene and the Control Region

Phylogenetic analysis was conducted for various populations of the Sorex minutissimus-S. yukonicus complex based on mitochondrial gene (cytochrome b and/or the control region) sequences. Sorex minutissimus was divided into some monophyletic groups in Eurasia; it was divided into 2 main groups, eastern and western Eurasian clades, based on combined data of the cytochrome b and the control region. Monophyly of shrews from Hokkaido-Sakhalin, Primorye, Mongolia-Transbaikalia, southeastern Finland was strongly supported respectively in most analyses. Sorex yukonicus was phylogenetically close to S. minutissimus in eastern Siberia. Some shrews from western and central Siberia were included in the clade of southeastern Finland. Also, most shrews from central-northern Finland and Norway made a clade close to but different from the southeastern Finland clade. This finding suggests that Fennoscandian shrews might consist of individuals which were recolonised from various refugia after the Last Glacial Maximum. Nucleotide diversity of shrews from Hokkaido and Alaska was low. Three regional groups in Kamchatka-Sakha, Sakhalin, and Mongolia-Transbaikalia tended to have medium nucleotide diversity. In contrast, shrews from Cisbaikalia-western Siberia and Fennoscandia had high nucleotide diversity. The S. minutissimus-S. hosonoi group appears to have experienceed a quit different biogeographic history from two shrews with similar ranges, the S. caecutiens-S. hosonoi group and S. tundrensis.

Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis

The distribution of freshwater taxa is a good biogeographic model to study pattern and process of vicariance and dispersal. The subfamily Leuciscinae (Cyprinidae, Teleostei) consists of many species distributed widely in Eurasia and North America. Leuciscinae have been divided into two phyletic groups, leuciscin and phoxinin. The phylogenetic relationships between major clades within the subfamily are poorly understood, largely because of the overwhelming diversity of the group. The origin of the Far Eastern phoxinin is an interesting question regarding the evolutionary history of Leuciscinae. Here we present phylogenetic analysis of 31 species of Leuciscinae and outgroups based on complete mitochondrial genome sequences to clarify the phylogenetic relationships and to infer the evolutionary history of the subfamily.Phylogenetic analysis suggests that the Far Eastern phoxinin species comprised the monophyletic clades Tribolodon, Pseudaspius, Oreoleuciscus and Far Eastern Phoxinus. The Far Eastern phoxinin clade was independent of other Leuciscinae lineages and was closer to North American phoxinins than European leuciscins. All of our analysis also suggested that leuciscins and phoxinins each constituted monophyletic groups. Divergence time estimation suggested that Leuciscinae species diverged from outgroups such as Tincinae to be 83.3million years ago (Mya) in the Late Cretaceous and leuciscin and phoxinin shared a common ancestor 70.7Mya. Radiation of Leuciscinae lineages occurred during the Late Cretaceous to Paleocene. This period also witnessed the radiation of tetrapods. Reconstruction of ancestral areas indicates Leuciscinae species originated within Europe. Leuciscin species evolved in Europe and the ancestor of phoxinin was distributed in North America. The Far Eastern phoxinins would have dispersed from North America to Far East across the Beringia land bridge. The present study suggests important roles for the continental rearrangements during the Late Cretaceous to form the present-day distribution of organisms. Furthermore, the Late Cretaceous biotic turnover influenced for the modern terrestrial biodiversity.

Two frog species or one? A multi-marker approach to assessing the distinctiveness of genetic lineages in the Northern Leopard Frog, Rana pipiens

A genetic boundary at the Mississippi River, USA, has been suggested for the Northern Leopard Frog, Rana pipiens, which was recently proposed for listing as federally threatened in the western USA. This suggestion was made on the basis of limited geographic sampling of a mitochondrial gene. However, mitochondrial DNA represents a very small part of the genome and is not necessarily indicative of patterns in nuclear DNA. We tested the hypothesis that eastern and western populations are separated by a distinct genetic boundary by sequencing mitochondrial DNA more extensively across the range, including focused sampling in the zone of hypothetical introgression, and by analyzing four nuclear sequences and seven microsatellite loci. We confirmed previous results that eastern and western populations have unique mitochondrial sequences that are deeply divergent (3.8 %) and which overlap only in a narrow region around the Mississippi River. Nuclear sequences also show divergent eastern and western lineages in some cases but with a broader zone of geographic overlap. Microsatellite data correspond closely to mitochondrial data, differing between east and west and changing abruptly near the Mississippi River. These data collectively demonstrate that eastern and western clades of this species introgress considerably in some markers but are distinct and defined by clear and narrow boundaries in others. We demonstrate that the Mississippi River forms an important, albeit somewhat permeable, boundary between genetic lineages in this species. This genetic boundary coincides with previously described discontinuities in morphological features.

Geographic variation of chloroplast DNA in Platycarya strobilacea (Juglandaceae)

Abstract The monotypic genus Platycarya (Juglandaceae) is one of the most widespread temperate tree species in East Asia. In this research, we implemented a phylogeographical study using chloroplast DNA (cpDNA) (psbA‐trnH and atpB‐rbcL intergenic spacer) sequences on Platycarya strobilacea, in order to identify the locations of the species’ main refugia and migration routes. A total of 180 individuals of P. stobilacea from 27 populations from China and Jeju Island (Korea) were collected. The results revealed that P. strobilacea had 35 haplotypes for the two intergenic spacers and high genetic diversity (hT= 0.926). This surprisingly high diversity of haplotypes indicates its long evolutionary history, which is in agreement with previous phylogenetic analyses and fossil records. Significant cpDNA population subdivision was detected (GST= 0.720; NST= 0.862), suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (NST > GST, P < 0.05). The construction of phylogenetic relationships of the 35 chlorotypes detected four major cpDNA clades. Divergence dating analyses using BEAST suggest that the divergence of the major cpDNA clades occurred before the Miocene. Demographic analysis indicated that the Eastern clade underwent localized demographic expansions. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggest the existence of multiple glacial refugia in most of its current range in China through Quaternary climatic oscillations.

Phylogeography of a Habitat Specialist with High Dispersal Capability: The Savi’s Warbler Locustella luscinioides

In order to describe the influence of Pleistocene glaciations on the genetic structure and demography of a highly mobile, but specialized, passerine, the Savi’s Warbler (Locustella luscinioides), mitochondrial DNA sequences (ND2) and microsatellites were analysed in c.330 individuals of 17 breeding and two wintering populations. Phylogenetic, population genetics and coalescent methods were used to describe the genetic structure, determine the timing of the major splits and model the demography of populations. Savi’s Warblers split from its sister species c.8 million years ago and have two major haplotype groups that diverged in the early/middle Pleistocene. One of these clades originated in the Balkans and is currently widespread, showing strong evidence for population expansion; whereas the other is restricted to Iberia and remained stable. Microsatellites agreed with a genetic break around the Pyrenees, but showed considerable introgression and a weaker genetic structure. Both genetic markers showed an isolation-by-distance pattern associated with the population expansion of the eastern clade. Breeding populations seem to be segregated at the wintering sites, but results on migratory connectivity are preliminary. Savi’s Warbler is the only known migratory bird species in which Iberian birds did not expand beyond the Pyrenees after the last glaciation. Despite the long period of independent evolution of western and eastern populations, complete introgression occurred when these groups met in Iberia. Mitochondrial sequences indicated the existence of refugia-within-refugia in the Iberian Peninsula during the last glacial period, which is surprising given the high dispersal capacity of this species. Plumage differences of eastern subspecies seemed to have evolved recently through natural selection, in agreement with the glacial expansion hypothesis. This study supports the great importance of the Iberian Peninsula and its role for the conservation of genetic variation.

Altingioxylon hainanensis sp. nov.: earliest fossil wood record of the family Altingiaceae in Eastern Asia and its implications for historical biogeography

A new species, Altingioxylon hainanensis, is described from the Eocene Changchang Formation of the Changchang Basin on Hainan Island, South China. It is the first record of a fossil wood assigned to Altingiaceae found in China, and the most ancient evidence of wood for this family in eastern Asia. The new species is similar to A. rhodoleioides, known since the Miocene in India and Java Island, and to Altingiahisauchii from the Miocene to Pliocene of Japan. The close resemblance between these species and Liquidambar sp., known from the Middle Miocene of western North America, provides additional evidence for the migration of their ancestors from Asia to North America across the Bering land bridge during the Miocene. Distinctions in ray sizes between the eastern Asian specimens and their contemporaries from Europe to Kazakhstan is suggested as a result of the divergence between the large eastern Asian clade and the North American–west Asian clade within Altingiaceae during the Eocene–Oligocene. The presence of crystals in ray cells may be considered an ancestral condition that persists in the eastern Asian lineages up to the extant Altingia and Semiliquidambar, but which was lost in other Altingiaceae in the course of evolution.

The Balkans and the colonization of Europe: the post‐glacial range expansion of the wild boar, Sus scrofa

AbstractAim We focus on the biogeographical role of the Balkan Peninsula as a glacial refugium and source of northward post‐glacial dispersal for many European taxa. Specifically, we analysed the genetic structure and variation of wild boar (Sus scrofa) samples primarily from Greece, a region that has repeatedly served as a glacial refugium within the Balkan Peninsula.Location Continental Greece, the Aegean island of Samos and Bulgaria.Methods We analysed wild boar samples from 18 localities. Samples from common domestic breeds were also examined to take into account interactions between wild and domesticated animals. Phylogenetic analyses were carried out on a 637‐bp fragment of the mitochondrial DNA control region in 200 wild boar and 27 domestic pigs. The sequences were also compared with 791 Eurasian wild boar and domestic pig D‐loop sequences obtained from GenBank.Results Ninety‐four haplotypes were identified in the European wild boar data set, of which 68 were found in the Balkan samples and assigned to two previously described clades: the E1 European and Near Eastern clades. All of the continental samples clustered in the E1 clade and the samples from Samos fell into the Near Eastern clade, consistent with the island’s proximity to Asia Minor. Intriguingly, 62 novel haplotypes were identified and are found exclusively in the Balkans. Only six haplotypes were shared between wild boar and domestic pigs.Main conclusions Our data reveal numerous novel and geographically restricted haplotypes in wild boar populations, suggesting the presence of separate refugia in the Balkans. Our analyses support the hypothesis of a post‐glacial wild boar expansion consistent with the leading edge model, north and west from modern day Greece, and suggest little maternal introgression of Near Eastern and domestic haplotypes into wild Balkan populations.

Cytochrome-bSequence Variation in Water Shrews (Sorex palustris) from Eastern and Western North America

Mitochondrial DNA sequence data for the cytochrome-b gene was used to assess genetic divergence among samples of Sorex palustris (Water Shrew) from eastern and western North America. Phylogenetic analysis revealed the presence of three previously observed clades—Cordilleran (S. p. navigator and S. p. brooksi), Coastal (S. bendirii), Boreal (S. p. palustris)—along with a novel Eastern clade (S. p. gloveralleni and/or S. p. albibarbis). Intraspecific divergence between the Boreal and Eastern clades was 3.42%, exceeding interspecific divergence between the Cordilleran and Coastal clades (3.35%). Application of the genetic species concept to the results of this study suggests that the Boreal and Eastern clades of Water Shrews warrant further investigation for recognition as two distinct sister species (i.e., S. palustris and S. albibarbis, respectively). Additional samples and analysis of nuclear markers will be required to substantiate this proposed taxonomic revision.

Multi locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events and rare out‐crossing

Pristionchus pacificus, recently established as a model organism in evolutionary biology, is a cosmopolitan nematode that has a necromenic association with scarab beetles. The diverse array of host beetle species and habitat types occupied by P.pacificus make it a good model for investigating local adaptation to novel environments. Presence of P.pacificus on La Réunion Island, a young volcanic island with a dynamic geological history and a wide variety of ecozones, facilitates such investigation in an island biogeographic setting. Microsatellite data from 20 markers and 223 strains and mitochondrial sequence data from 272 strains reveal rich genetic diversity among La Réunion P.pacificus isolates, shaped by differentially timed introductions from diverse sources and in association with different beetle species. Distinctions between volcanic zones and between arid western and wet eastern climatic zones have likely limited westward dispersal of recently colonized lineages and maintained a genetic distinction between eastern and western clades. The highly selfing lifestyle of P.pacificus contributes to the strong fine-scale population structure detected, with each beetle host harbouring strongly differentiated assemblages of strains. Periodic out-crossing generates admixture between genetically diverse lineages, creating a diverse array of allelic combinations likely to increase the evolutionary potential of the species and facilitate adaptation to local environments and beetle hosts.

The evolution and age of populations of Scaphinotus petersi Roeschke on Arizona Sky Islands (Coleoptera, Carabidae, Cychrini).

Populations of the ground beetle Scaphinotus petersi are isolated in subalpine conifer forest habitats on mountain ranges or Sky Islands in southeastern Arizona. Previous work on this species has suggested these populations have been isolated since the last post-glacial maximum times as warming caused this cool adapted species to retreat to high elevations. To test this hypothesis, we inferred the phylogeny from mitochondrial DNA sequence data from several Arizona Sky Island populations of Scaphinotus petersi and estimated the divergence time of the currently isolated populations. We found two major clades of Scaphinotus petersi, an eastern clade and a western group. Our results indicated most mountain ranges form clades except the Huachucas, which are polyphyletic and the Santa Catalinas, which are paraphyletic. We estimated the Pinaleño population is much older than the last glacial maximum, but the Huachuca and Pinal populations may have been fragmented from the Santa Catalina population since the post-glacial maximum times.

Diversification within the Mexican Vole (Microtus mexicanus) and the Role of Post-Pleistocene Climate Change

To examine the partitioning of genetic variation within the Mexican vole (Microtus mexicanus), we analyzed variation within the cytochrome b (cytb, ca. 953 bp) from 44 samples of the Mexican vole from the mountains of the southwestern United States and Mexico. Phylogeographic analyses demonstrated strong support for a western clade and an eastern clade, corresponding to the Sierra Madre Occidental and mountains of the southwestern United States (western clade) and the Sierra Madre Oriental and the Sierra Madre del Sur (eastern clade). Levels of genetic distinctiveness among vole populations in Mexico and the southwestern United States support recognition of the Mogollon vole (Microtus mogollonensis). Estimates of lineage divergence suggested an older divergence for populations in Mexico and a more recent divergence for the presumptive M. mogollonensis. Ecological analyses demonstrated a distinct climate niche between vole lineages in the Southwest and Mexico, which indicated the possible role of environmental variation in diversification of the Mexican vole. A similar pattern of climatic separation was also demonstrated between clades of the codistributed taxa Sigmodon hispidus, Neotoma mexicana, and Peromyscus truei, suggesting a broader role for climatic variation in the origin and maintenance of the region's biodiversity.

Genetic variation and seasonal migratory connectivity in Wilson’s warblers (Wilsonia pusilla): species-level differences in nuclear DNA between western and eastern populations

There is growing interest in understanding patterns of seasonal migratory connectivity between breeding and wintering sites, both because differences in migratory behaviour can be associated with population differentiation and because knowledge of migratory connectivity is essential for understanding the ecology, evolution and conservation of migratory species. We present the first broad survey of geographic variation in the nuclear genome of breeding and wintering Wilson's warblers (Wilsonia pusilla), which have previously served as a research system for the study of whether genetic markers and isotopes can reveal patterns of migratory connectivity. Using 153 samples surveyed at up to 257 variable amplified fragment length polymorphism markers, we show that Wilson's warblers consist of highly distinct western and eastern breeding groups, with all winter samples grouping with the western breeding group. Within the west, there is weak geographic differentiation, at a level insufficient for use in the assignment of wintering samples to specific areas. The distinctiveness of western and eastern genetic groups, with no known intermediates, strongly suggests that these two groups are cryptic species. Analysis of mitochondrial cytochrome b sequence variation shows that the estimated coalescence time between western and eastern clades is approximately 2.3 Ma, a surprisingly old time of divergence that is more typical of distinct species than of subspecies. Given their morphological similarity but strong genetic differences, western and eastern Wilson's warblers present a likely case of association between divergence in migratory behaviour and the process of speciation.

Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America’s Great Basin

AimThe rodent genus Microdipodops (kangaroo mice) includes two sand-obligate endemics of the Great Basin Desert: M. megacephalus and M. pallidus. The dark kangaroo mouse, M. megacephalus, is distributed throughout the Great Basin and our principal aims were to formulate phylogenetic hypotheses for this taxon and make phylogeographical comparisons with its congener.LocationThe Great Basin Desert of western North America.MethodsDNA sequence data from three mitochondrial genes were examined from 186 individuals of M. megacephalus, representing 47 general localities. Phylogenetic inference was used to analyse the sequence data. Directional analysis of phylogeographical patterns was used to examine haplotype sharing patterns and recover routes of gene exchange. Haplotype–area curves were constructed to evaluate the relationship between genetic variation and distributional island size for M. megacephalus and M. pallidus.ResultsMicrodipodops megacephalus is a rare desert rodent (trapping success was 2.67%). Temporal comparison of trapping data shows that kangaroo mice are becoming less abundant in the study area. The distribution has changed slightly since the 1930s but many northern populations now appear to be small, fragmented, or locally extinct. Four principal phylogroups (the Idaho isolate and the western, central and eastern clades) are evident; mean sequence divergence between phylogroups for cytochrome b is c. 8%. Data from haplotype sharing show two trends: a north–south trend and a web-shaped trend. Analyses of haplotype–area curves reveal significant positive relationships.Main conclusionsThe four phylogroups of M. megacephalus appear to represent morphologically cryptic species; in comparison, a companion study revealed two cryptic lineages in M. pallidus. Estimated divergence times of the principal clades of M. megacephalus (c. 2–4 Ma) indicate that these kangaroo mice were Pleistocene invaders into the Great Basin coincident with the formation of sandy habitats. The north–south and web patterns from directional analyses reveal past routes of gene flow and provide evidence for source–sink population regulation. The web pattern was not seen in the companion study of M. pallidus. Significant haplotype–area curves indicate that the distributional islands are now in approximate genetic equilibrium. The patterns described here are potentially useful to conservation biologists and wildlife managers and may serve as a model for other sand-obligate organisms of the Great Basin.

Population estimation and monitoring of an endangered lagomorph

We conducted the most intensive estimate of the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) metapopulation to date using pellet surveys and capture–recapture methodology. We livetrapped 83 rabbits, evaluated 5 closed population models, and selected the model that best represented the data. We considered the variation in behavioral response model the best model and correlated (r2 = 0.913) its patch population estimates to patch pellet densities. From the prediction equation, we generated a range-wide metapopulation estimate of 317 rabbits, a western clade population of 257 rabbits, an eastern clade population of 25 rabbits, and translocated marsh rabbit populations of 35 and zero on Little Pine and Water keys, respectively. A subset of patches whose marsh rabbit subpopulations were last estimated in 1993 exhibited a 46% decline in abundance over 15 yr. Due to the low estimate of the eastern clade population, special effort should be initiated to avoid loss of genetic diversity. The prediction equation suffers from limited data at high pellet densities, patches with ≥5 pellets/m2. Future studies should investigate if the slope of the regression is indeed near 1 by sampling patches across the range of pellet densities, especially those with ≥5 pellets/m2. The equation provides managers a quick, efficient, and noninvasive method to estimate marsh rabbit abundance from pellet counts but the confidence of predicted rabbit densities from high pellet density patches is low. © 2011 The Wildlife Society

Extrinsic and intrinsic influences on the phylogeography of the Austrocochlea constricta species group

Although extrinsic factors, such as oceanic currents and isolation induced by sea level maxima during Plio-Pleistocene glacial cycles, are often suggested as principal determinants of marine phylogeography, they are not always complete explanations. The counterexamples to predominant phylogeographic patterns in southeastern Australia suggest for example, that intrinsic factors such a habitat preference or reproductive mode can have significant influence. We collected DNA sequences from mitochondrial cytochrome c oxidase I (COI) and two nuclear gene introns from the Austrocochlea constricta species group to determine whether its porcata and constricta phenotypes are genetically distinguishable, to examine the phylogeographic effects of the Bassian Isthmus landbridge formed between Tasmania and Victoria during glacial maxima, and to investigate the importance of intrinsic factors in structuring its genetic variability. No fixed genetic differences between the porcata and constricta phenotypes were identified in any gene so the number of species comprised by the group cannot yet be determined. The two major clades recovered in COI analyses were respectively found principally east or west of the Bassian Isthmus. A. constricta is the first lecithotrophic or estuarine invertebrate known to show this pattern. There were no fixed differences, for any of the three genes, between specimens from estuarine and marine populations within either the eastern or western COI clades. Other intrinsic factors such as breeding period (possibly) and larval type (probably) may play roles in modulating phylogeographic patterns.

Molecular genetic evidence of a deep phylogenetic discontinuity between the asian and european races of pygmy wood mouse based on the mitochondrial cytochrome b gene variation

The variation of mitochondrial DNA (mtDNA) cytochrome b gene sequences of pygmy wood mouse Sylvaemus uralensis (Pallas, 1811) from local populations of European Russia, West Siberia, and neighboring countries (Moldova, Kazakhstan, Uzbekistan, and Turkmenistan) has been studied. Phylogenetic analysis based on our results and GenBank data revealed two clusters of haplotypes: the Western clade, which was reliably subdivided into two sequence groups, and the Eastern clade with no significant differentiation. The clusters corresponded exactly to the European and Asian races of pygmy wood mouse recognized previously on the basis of biochemical and karyotypic variation. We suppose that the Asian race can be considered as an independent allopatric species. This concept is supported by the following evidence: the high interrace divergence level suggesting more than 1 Ma of divergent evolution, the absence of common haplotypes and the hiatus between the main peaks of the mismatch distribution, difference in the codon usage frequencies, fixed nucleotide substitutions in cyt b, as well as different amino acid sequences of cytochrome b. Only specimens of the western phylogenetic lineage should be classified as S. uralensis (Pallas, 1811), while S. tokmak, according to its first description (Severtsov, 1873), may be considered as the species uniting specimens of the eastern phylogenetic lineage.

Relics of the Europe’s warm past: Phylogeography of the Aesculapian snake

Understanding how species responded to past climate change can provide information about how they may respond to the current global warming. Here we show how a European reptile species responded to the last natural global warming event at the Pleistocene–Holocene transition that led to the Holocene climatic optimum approximately 5000–8000 years ago. The Aesculapian snake, Zamenis longissimus, is a thermophilous species whose present-day distribution in the southern half of Europe is a remnant of much wider range during the Holocene climatic optimum when populations occurred as far north as Denmark. These northern populations went extinct as the climate cooled, and presently the species is extinct from all central Europe, except few relic populations in locally suitable microhabitats in Germany and the Czech Republic. Our phylogenetic and demographic analyses identified two major clades that expanded from their respective western and eastern refugia after the last glacial maximum (18,000–23,000 years ago) and contributed approximately equally to the present range. Snakes from the relic northern populations carried the Eastern clade, showing that it was primarily the snakes from the eastern, probably Balkan, refugium that occupied the central and northern Europe during the Holocene climatic optimum. Two small, deep-branching clades were identified in near the Black Sea and in Greece. These clades provide evidence for two additional refugia, which did not successfully contribute to the colonization of Europe. If, as our results suggest, some populations responded to the mid-Holocene global warming by shifting their ranges further north than other populations of the same species, knowing what populations were able to expand in different species may provide information about what populations will be important for the species’ ability to cope with the current global warming.